sc2marker

We tried to use sc2marker to find the minimal protein markers to differentiate a certain cell type from the rest of the clusters.

There are 24 cell types in total in this dataset. Each cell type was provided a list of markers and their corresponding ranking scores. TP: true positives, FP: false positives, TN: true negatives, FN: false negatives. The direction indicates whether the marker is highly (+) / lowly(-) expressed in the specific cell type compared to the rest groups. The x-axis in the ridge plot is in log2(x+1) scale. The red dashed line indicatesd the ranking score for each gene.

Cluster: non-classical monocyte

Table

celltype <- "non-classical monocyte"
markers <- markers.all[[celltype]]; markers$`FP details`=NA
get_antibody(markers, org = "human")

Ridge

plot_ridge2(scrna, id = celltype, genes = markers[1:6,]$gene, 
           aggr.other = FALSE, ncol = 3, assay = "ADT", slot = "data")

Cluster: classical monocyte

Table

celltype <- "classical monocyte"
markers <- markers.all[[celltype]]; markers$`FP details`=NA
get_antibody(markers, org = "human")

Ridge

plot_ridge2(scrna, id = celltype, genes = markers[1:6,]$gene, 
           aggr.other = FALSE, ncol = 3, assay = "ADT", slot = "data")

Cluster: CD16-positive, CD56-dim natural killer cell, human

Table

celltype <- "CD16-positive, CD56-dim natural killer cell, human"
markers <- markers.all[[celltype]]; markers$`FP details`=NA
get_antibody(markers, org = "human")

Ridge

plot_ridge2(scrna, id = celltype, genes = markers[1:6,]$gene, 
           aggr.other = FALSE, ncol = 3, assay = "ADT", slot = "data")

Cluster: natural killer cell

Table

celltype <- "natural killer cell"
markers <- markers.all[[celltype]]; markers$`FP details`=NA
get_antibody(markers, org = "human")

Ridge

plot_ridge2(scrna, id = celltype, genes = markers[1:6,]$gene, 
           aggr.other = FALSE, ncol = 3, assay = "ADT", slot = "data")

Cluster: plasmacytoid dendritic cell

Table

celltype <- "plasmacytoid dendritic cell"
markers <- markers.all[[celltype]]; markers$`FP details`=NA
get_antibody(markers, org = "human")

Ridge

plot_ridge2(scrna, id = celltype, genes = markers[1:6,]$gene, 
           aggr.other = FALSE, ncol = 3, assay = "ADT", slot = "data")

Cluster: conventional dendritic cell

Table

celltype <- "conventional dendritic cell"
markers <- markers.all[[celltype]]; markers$`FP details`=NA
get_antibody(markers, org = "human")

Ridge

plot_ridge2(scrna, id = celltype, genes = markers[1:6,]$gene, 
           aggr.other = FALSE, ncol = 3, assay = "ADT", slot = "data")

Cluster: platelet

Table

celltype <- "platelet"
markers <- markers.all[[celltype]]; markers$`FP details`=NA
get_antibody(markers, org = "human")

Ridge

plot_ridge2(scrna, id = celltype, genes = markers[1:6,]$gene, 
           aggr.other = FALSE, ncol = 3, assay = "ADT", slot = "data")

Cluster: CD16-negative, CD56-bright natural killer cell, human

Table

celltype <- "CD16-negative, CD56-bright natural killer cell, human"
markers <- markers.all[[celltype]]; markers$`FP details`=NA
get_antibody(markers, org = "human")

Ridge

plot_ridge2(scrna, id = celltype, genes = markers[1:6,]$gene, 
           aggr.other = FALSE, ncol = 3, assay = "ADT", slot = "data")

Cluster: granulocyte

Table

celltype <- "granulocyte"
markers <- markers.all[[celltype]]; markers$`FP details`=NA
get_antibody(markers, org = "human")

Ridge

plot_ridge2(scrna, id = celltype, genes = markers[1:6,]$gene, 
           aggr.other = FALSE, ncol = 3, assay = "ADT", slot = "data")

Cluster: intermediate monocyte

Table

celltype <- "intermediate monocyte"
markers <- markers.all[[celltype]]; markers$`FP details`=NA
get_antibody(markers, org = "human")

Ridge

plot_ridge2(scrna, id = celltype, genes = markers[1:6,]$gene, 
           aggr.other = FALSE, ncol = 3, assay = "ADT", slot = "data")

Cluster: naive B cell

Table

celltype <- "naive B cell"
markers <- markers.all[[celltype]]; markers$`FP details`=NA
get_antibody(markers, org = "human")

Ridge

plot_ridge2(scrna, id = celltype, genes = markers[1:6,]$gene, 
           aggr.other = FALSE, ncol = 3, assay = "ADT", slot = "data")

Cluster: memory B cell

Table

celltype <- "memory B cell"
markers <- markers.all[[celltype]]; markers$`FP details`=NA
get_antibody(markers, org = "human")

Ridge

plot_ridge2(scrna, id = celltype, genes = markers[1:6,]$gene, 
           aggr.other = FALSE, ncol = 3, assay = "ADT", slot = "data")

Cluster: gamma-delta T cell

Table

celltype <- "gamma-delta T cell"
markers <- markers.all[[celltype]]; markers$`FP details`=NA
get_antibody(markers, org = "human")

Ridge

plot_ridge2(scrna, id = celltype, genes = markers[1:6,]$gene, 
           aggr.other = FALSE, ncol = 3, assay = "ADT", slot = "data")

Cluster: plasmablast

Table

celltype <- "plasmablast"
markers <- markers.all[[celltype]]; markers$`FP details`=NA
get_antibody(markers, org = "human")

Ridge

plot_ridge2(scrna, id = celltype, genes = markers[1:6,]$gene, 
           aggr.other = FALSE, ncol = 3, assay = "ADT", slot = "data")

Cluster: regulatory T cell

Table

celltype <- "regulatory T cell"
markers <- markers.all[[celltype]]; markers$`FP details`=NA
get_antibody(markers, org = "human")

Ridge

plot_ridge2(scrna, id = celltype, genes = markers[1:6,]$gene, 
           aggr.other = FALSE, ncol = 3, assay = "ADT", slot = "data")

Cluster: CD4-positive, alpha-beta memory T cell

Table

celltype <- "CD4-positive, alpha-beta memory T cell"
markers <- markers.all[[celltype]]; markers$`FP details`=NA
get_antibody(markers, org = "human")

Ridge

plot_ridge2(scrna, id = celltype, genes = markers[1:6,]$gene, 
           aggr.other = FALSE, ncol = 3, assay = "ADT", slot = "data")

Cluster: CD8-positive, alpha-beta memory T cell

Table

celltype <- "CD8-positive, alpha-beta memory T cell"
markers <- markers.all[[celltype]]; markers$`FP details`=NA
get_antibody(markers, org = "human")

Ridge

plot_ridge2(scrna, id = celltype, genes = markers[1:6,]$gene, 
           aggr.other = FALSE, ncol = 3, assay = "ADT", slot = "data")

Cluster: naive thymus-derived CD8-positive, alpha-beta T cell

Table

celltype <- "naive thymus-derived CD8-positive, alpha-beta T cell"
markers <- markers.all[[celltype]]; markers$`FP details`=NA
get_antibody(markers, org = "human")

Ridge

plot_ridge2(scrna, id = celltype, genes = markers[1:6,]$gene, 
           aggr.other = FALSE, ncol = 3, assay = "ADT", slot = "data")

Cluster: naive thymus-derived CD4-positive, alpha-beta T cell

Table

celltype <- "naive thymus-derived CD4-positive, alpha-beta T cell"
markers <- markers.all[[celltype]]; markers$`FP details`=NA
get_antibody(markers, org = "human")

Ridge

plot_ridge2(scrna, id = celltype, genes = markers[1:6,]$gene, 
           aggr.other = FALSE, ncol = 3, assay = "ADT", slot = "data")

Cluster: mucosal invariant T cell

Table

celltype <- "mucosal invariant T cell"
markers <- markers.all[[celltype]]; markers$`FP details`=NA
get_antibody(markers, org = "human")

Ridge

plot_ridge2(scrna, id = celltype, genes = markers[1:6,]$gene, 
           aggr.other = FALSE, ncol = 3, assay = "ADT", slot = "data")

Cluster: memory T cell

Table

celltype <- "memory T cell"
markers <- markers.all[[celltype]]; markers$`FP details`=NA
get_antibody(markers, org = "human")

Ridge

plot_ridge2(scrna, id = celltype, genes = markers[1:6,]$gene, 
           aggr.other = FALSE, ncol = 3, assay = "ADT", slot = "data")

Cluster: double-positive, alpha-beta thymocyte

Table

celltype <- "double-positive, alpha-beta thymocyte"
markers <- markers.all[[celltype]]; markers$`FP details`=NA
get_antibody(markers, org = "human")

Ridge

plot_ridge2(scrna, id = celltype, genes = markers[1:6,]$gene, 
           aggr.other = FALSE, ncol = 3, assay = "ADT", slot = "data")

Cluster: double negative thymocyte

Table

celltype <- "double negative thymocyte"
markers <- markers.all[[celltype]]; markers$`FP details`=NA
get_antibody(markers, org = "human")

Ridge

plot_ridge2(scrna, id = celltype, genes = markers[1:6,]$gene, 
           aggr.other = FALSE, ncol = 3, assay = "ADT", slot = "data")

Cluster: T cell

Table

celltype <- "T cell"
markers <- markers.all[[celltype]]; markers$`FP details`=NA
get_antibody(markers, org = "human")

Ridge

plot_ridge2(scrna, id = celltype, genes = markers[1:6,]$gene, 
           aggr.other = FALSE, ncol = 3, assay = "ADT", slot = "data")